RAF East Kirkby served also as the headquarters of No 5 (Bomber) Group RAF in command of satellite stations at RAF Strubby, RAF Spilsby, RAF Hemswell and RAF Manby.

On April 17 1945, near the end of the Second World War, a 57 Squadron Lancaster was being loaded with bombs when a fully armed 1,000lb bomb was unintentionally dropped onto the tarmac. Because the bomb had had its fuse inserted it detonated, setting off the rest of the Lancaster's bombload. A massive explosion killed three airmen, injured 16 others, wrote off six other Lancasters beyond repair and badly damaged a nearby aircraft hangar.

The final wartime raid from East Kirkby was flown on 25 April 1945. In total, 212 operations were carried out during the war, from which 121 Lancasters did not return. Another 29 aircraft were lost due to operational crashes or accidents.

630 Squadron disbanded in July that year and its place was taken by No. 460 Squadron RAAF from RAF Binbrook. This squadron joined No. 57 for transfer to the Far East as part of Tiger Force. In the 1950s, the base was used by the USAF for Air Rescue squadrons for four years. The station (code name Silksheen) closed in 1958. It was sold by the government in 1964.